alignment.js/components/ScaffoldViewer.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/

"use strict";

Object.defineProperty(exports, "__esModule", {
  value: true
});
exports["default"] = void 0;

var _react = _interopRequireWildcard(require("react"));

var _fasta = _interopRequireDefault(require("./../helpers/fasta"));

var _computeLabelWidth = _interopRequireDefault(require("../helpers/computeLabelWidth"));

var _BaseAlignment = _interopRequireDefault(require("./BaseAlignment.js"));

var _SiteAxis = _interopRequireDefault(require("./SiteAxis.js"));

var _SequenceAxis = _interopRequireDefault(require("./SequenceAxis.js"));

var _Scaffold = _interopRequireDefault(require("./Scaffold.js"));

var _scroll_broadcaster = _interopRequireDefault(require("./../helpers/scroll_broadcaster"));

var _format = _interopRequireDefault(require("../helpers/format"));

var _colors = require("./../helpers/colors");

function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { "default": obj }; }

function _getRequireWildcardCache() { if (typeof WeakMap !== "function") return null; var cache = new WeakMap(); _getRequireWildcardCache = function _getRequireWildcardCache() { return cache; }; return cache; }

function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { "default": obj }; } var cache = _getRequireWildcardCache(); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj["default"] = obj; if (cache) { cache.set(obj, newObj); } return newObj; }

function _typeof(obj) { "@babel/helpers - typeof"; if (typeof Symbol === "function" && typeof Symbol.iterator === "symbol") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; } return _typeof(obj); }

function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } }

function _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }

function _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }

function _createSuper(Derived) { return function () { var Super = _getPrototypeOf(Derived), result; if (_isNativeReflectConstruct()) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }

function _possibleConstructorReturn(self, call) { if (call && (_typeof(call) === "object" || typeof call === "function")) { return call; } return _assertThisInitialized(self); }

function _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError("this hasn't been initialised - super() hasn't been called"); } return self; }

function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }

function _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }

function _inherits(subClass, superClass) { if (typeof superClass !== "function" && superClass !== null) { throw new TypeError("Super expression must either be null or a function"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }

function _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }

var ScaffoldViewer = /*#__PURE__*/function (_Component) {
  _inherits(ScaffoldViewer, _Component);

  var _super = _createSuper(ScaffoldViewer);

  function ScaffoldViewer(props) {
    var _this;

    _classCallCheck(this, ScaffoldViewer);

    _this = _super.call(this, props);
    _this.label_width = 200;

    _this.initialize(_this.props);

    return _this;
  }

  _createClass(ScaffoldViewer, [{
    key: "setScrollingEvents",
    value: function setScrollingEvents(props) {
      if (props.fasta) {
        var alignment_width = props.alignment_width,
            alignment_height = props.alignment_height;
        var full_pixel_width = this.full_pixel_width,
            full_pixel_height = this.full_pixel_height;
        this.scroll_broadcaster = new _scroll_broadcaster["default"]({
          width: full_pixel_width,
          height: full_pixel_height,
          x_pad: alignment_width,
          y_pad: alignment_height,
          x_pixel: this.x_pixel,
          y_pixel: this.y_pixel,
          bidirectional: ["alignmentjs-reference-alignment", "alignmentjs-alignment", "alignmentjs-axis-div", "alignmentjs-labels-div", "alignmentjs-scaffold-div"]
        });
      }
    }
  }, {
    key: "componentWillUpdate",
    value: function componentWillUpdate(nextProps) {
      this.initialize(nextProps);
    }
  }, {
    key: "initialize",
    value: function initialize(props) {
      if (props.fasta) {
        var fasta = props.fasta,
            site_size = props.site_size;
        this.sequence_data = (0, _fasta["default"])(fasta);
        var sequence_data = this.sequence_data;
        var label_padding = this.props.label_padding;
        this.label_width = (0, _computeLabelWidth["default"])(sequence_data, label_padding);
        this.full_pixel_width = site_size * sequence_data.number_of_sites;
        this.full_pixel_height = site_size * (sequence_data.number_of_sequences - 1);
      }

      this.setScrollingEvents(props);
    }
  }, {
    key: "render",
    value: function render() {
      if (!this.sequence_data) {
        return /*#__PURE__*/_react["default"].createElement("div", {
          style: container_style,
          id: "alignmentjs-main-div"
        });
      }

      var _this$props = this.props,
          alignment_width = _this$props.alignment_width,
          alignment_height = _this$props.alignment_height,
          scaffold_width = _this$props.scaffold_width,
          container_style = {
        display: "grid",
        gridTemplateColumns: (0, _format["default"])([this.label_width, alignment_width, scaffold_width]),
        gridTemplateRows: (0, _format["default"])([20, 20, alignment_height])
      },
          reference_sequence_data = this.sequence_data.slice(0, 1),
          remaining_sequence_data = this.sequence_data.slice(1);
      return /*#__PURE__*/_react["default"].createElement("div", {
        style: container_style,
        id: "alignmentjs-main-div"
      }, /*#__PURE__*/_react["default"].createElement("div", {
        id: "alignmentjs-axis-placeholder1"
      }), /*#__PURE__*/_react["default"].createElement(_SiteAxis["default"], {
        width: alignment_width,
        height: 20,
        sequence_data: this.sequence_data,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement("div", {
        id: "alignmentjs-axis-placeholder2"
      }), /*#__PURE__*/_react["default"].createElement(_SequenceAxis["default"], {
        width: this.label_width,
        height: this.props.site_size,
        sequence_data: reference_sequence_data,
        site_size: this.props.site_size,
        id: "alignmentjs-reference",
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_BaseAlignment["default"], {
        width: alignment_width,
        height: this.props.site_size,
        sequence_data: reference_sequence_data,
        site_size: this.props.site_size,
        id: "alignmentjs-reference",
        disableVerticalScrolling: true,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement("div", {
        id: "alignmentjs-reference-placeholder"
      }), /*#__PURE__*/_react["default"].createElement(_SequenceAxis["default"], {
        width: this.label_width,
        height: 800,
        sequence_data: remaining_sequence_data,
        site_size: this.props.site_size,
        y_pixel: this.y_pixel,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_BaseAlignment["default"], {
        width: alignment_width,
        height: 800,
        sequence_data: remaining_sequence_data,
        site_size: this.props.site_size,
        scroll_broadcaster: this.scroll_broadcaster
      }), /*#__PURE__*/_react["default"].createElement(_Scaffold["default"], {
        width: scaffold_width,
        height: 800,
        sequence_data: remaining_sequence_data,
        scroll_broadcaster: this.scroll_broadcaster
      }));
    }
  }]);

  return ScaffoldViewer;
}(_react.Component);

ScaffoldViewer.defaultProps = {
  site_color: _colors.nucleotide_color,
  text_color: _colors.nucleotide_text_color,
  site_size: 20,
  label_padding: 10,
  axis_height: 20,
  alignment_width: 600,
  alignment_height: 800,
  scaffold_width: 400
};
var _default = ScaffoldViewer;
exports["default"] = _default;